Ok, i'm a bit further into the game now, got a few gems, and a new type of stone(which apparently contains gems, how do i get them out?)
...With a pick?
If it's cut gems you're after, then you need a jeweler's workshop and a dwarf with the Gem Cutting job. The menu there is different to the other workshops, but it's self-explanatory. Or you could just order them off the dwarven caravan, as gem cutters sometimes produce crafts or large gems instead of the usual handful of cut gems. Very unhelpful if they were needed for a mood.
Overview of fortress: http://mkv25.net/dfma/map-6589-toweroftime
Anything special i should improve or add?
Is that fat rendered? If not, do that and then cook it all up into prepared meals (use the Kitchen screen to tell dwarves what to cook and brew. It's on the status screen (z)). Split your refuse pile into two physically separate sections -- one for bones, shells, and skulls, and one for everything else. This stops miasma from reaching passers-by. Mostly the fortress needs to be more efficient with storage. The seeds aren't in bags, the food isn't condensed into meals, and the bonecrafter's materials are sitting there doing nothing.
For defence, a lever-linked bridge over a channel on the north and west entrances will come in handy if you want to retreat. Since the level below the south entrance is dug you won't be able to do that there, and in your place I'd remove the door and wall it up.